+Open data
-Basic information
Entry | Database: PDB / ID: 1m0s | ||||||
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Title | NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID IR21) | ||||||
Components | Ribose-5-Phosphate Isomerase A | ||||||
Keywords | ISOMERASE / D-Ribose 5-phosphate Isomerase / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / IR21 / Haemophilus influenzae / structural genomics / PSI / Protein Structure Initiative / NESG | ||||||
Function / homology | Function and homology information D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Das, K. / Xiao, R. / Acton, T. / Montelione, G. / Arnold, E. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: D-RIBOSE-5-PHOSPHATE ISOMERASE, IR21 Authors: Das, K. / Xiao, R. / Acton, T. / Montelione, G. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0s.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0s.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0s ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0s | HTTPS FTP |
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-Related structure data
Related structure data | 1lkzS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23172.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: RPIA / Production host: Escherichia coli (E. coli) / References: UniProt: P44725, ribose-5-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.89 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2002 |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 37892 / % possible obs: 92.6 % / Observed criterion σ(I): -1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3663 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LKZ Resolution: 1.9→25.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1881744.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.0194 Å2 / ksol: 0.347824 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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